Police closed the stretch of the local road and stopped traffic from using the above southbound span during their investigation.
Drivers already on the bridge got out of their stopped vehicles as they waited for police to investigate the SUV.
Northbound traffic was permitted to use the Throgs Neck Bridge travel into the Bronx.
The Willets Point Boulevard closure also diverted local bus traffic through the area.
Police said they had no reason to think the SUV was a threat, but were acting out of an abundance of caution.
The bridge was reopened shortly after 7:30 a.m.